Chapter 5: The Content of the Genome

 Genomes can be mapped by a number of techniques, including linkage and restriction maps and
DNA sequencing.
o Linkage maps are based on the frequency of recombination between genetic markers;
restriction maps are based on the physical distances between markers.
 Genetic polymorphism is observed in individual genomes due to the coexistence of multiple
alleles at a given locus.
o Polymorphism may be detected at the phenotypic level when a sequence affects gene
function, at the restriction fragment level when it affects a restriction enzyme target
site, and at the sequence level by direct analysis of DNA.
o The alleles of a gene show extensive polymorphism at the sequence level, but many
sequence changes do not affect function.
 Restriction fragment length polymorphisms (RFLPs; a difference in restriction maps between
two individuals) and single nucleotide polymorphisms (SNPs) can be very useful for genetic
mapping of disease genes for which a genetic linkage is known but for which the gene has not
yet been identified.
o They are also useful for establishing parent–offspring relationships and DNA
fingerprinting.
o Every individual has a unique set of SNPs and RFLPs in any given region, called a
haplotype.
 Genomes tend to be much larger than what is needed to encode the necessary proteins and
other functions, and in higher eukaryotes a large amount of repetitive DNA elements is
common.
o A significant part of repetitive DNA consists of transposons, short sequences of DNA
that have the ability to move to new locations in the genome and/or to make additional
copies of themselves.
 Exon regions of genes tend to be conserved, whereas introns and intergenic regions tend to not
be conserved.
o Observation of conserved sequenced in different organisms can help identify coding
regions.
o The conservation of exons can be used to identify protein-coding genes in diseases such
as Duchenne muscular dystrophy (DMD).
o Techniques such as chromosome walking and exon trapping can also be used to identify
disease genes.
 Reverse transcriptase PCR (RT-PCR) and expressed sequence tag (EST) analysis can be used to
confirm that a particular DNA sequence is indeed transcribed, and is not a pseudogene.
o Comparison between different genomes can help confirm gene prediction.
 Mitochondria and chloroplasts contain extranuclear genomes with characteristics of bacterial
genomes, reflective of their endosymbiotic origin.
o They have genomes that show non-Mendelian inheritance and are typically maternally
inherited (all copies of the organelle genome are inherited solely from the female
parent).
o Comparisons of mitochondrial DNA sequences in a range of human populations allow an
evolutionary tree to be constructed that implies that human mitochondrial DNA is
descended from a single population that lived in Africa ~200,000 years ago.
  Organelle genomes are usually (but not always) circular molecules of DNA that encode for some
(but not all) of the proteins used in the organelle.
o Chloroplast genomes vary in size, but are large enough to encode 50 to 100 proteins as
well as the rRNAs and tRNAs.
o Mitochondrial genomes range widely in size between different classes of organisms,
being very compact in animals and very large in fungi and plants.
o Animal mtDNA genomes are highly compact and conserved except for the variable D-
loop region involved in replication and transcription.
 Phylogenetic analysis of these genome sequences show close relationships with bacterial
genomes, supporting an endosymbiotic origin for these organelles from a bacterial ancestor.

Interactive Media
Chapter 5: The Content of the Genome

Law and the Genetics of Identity: The Science of DNA Fingerprinting

Good presentation on the basics and applications of forensic DNA science

Understanding the Human Genome Project

Interactive website to learn about the human genome project

Sequence for yourself

Nova website to learn about DNA sequence analysis
James Watson's personal genome sequence
Actual genome sequence of James D Watson of double helix fame.
Experimental Gene Discovery Suite
Website for gene discovery and analysis